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0  structures 213  species 0  interactions 292  sequences 3  architectures

Family: Folliculin (PF11704)

Summary: Vesicle coat protein involved in Golgi to plasma membrane transport

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Vesicle coat protein involved in Golgi to plasma membrane transport Provide feedback

In yeast cells this family functions in the regulated delivery of Gap1p (a general amino acid permease) to the cell surface, perhaps as a component of a post-Golgi secretory-vesicle coat complex [1]. Birt-Hogg-Dube (BHD)4 syndrome is an autosomal dominant disorder characterised by hamartomas of skin follicles, lung cysts, spontaneous pneumothorax, and renal cell carcinoma. Folliculin is the protein from the BHD4 gene and is found to have no significant homology to any other human proteins. It is expressed in most tissues. These same symptoms also occur in TSC or tuberous sclerosis complex, suggesting that the same pathway is involved, and it is likely that the target is the down-stream Tor2 - an essential gene. Folliculin appears to bind Tor2, and down-regulation of Tor2 activity leads to up-regulation of nitrogen responsive genes including membrane transporters and amino acid permeases [2].

Literature references

  1. Roberg KJ, Bickel S, Rowley N, Kaiser CA; , Genetics. 1997;147:1569-1584.: Control of amino acid permease sorting in the late secretory pathway of Saccharomyces cerevisiae by SEC13, LST4, LST7 and LST8. PUBMED:9409822 EPMC:9409822

  2. van Slegtenhorst M, Khabibullin D, Hartman TR, Nicolas E, Kruger WD, Henske EP; , J Biol Chem. 2007;282:24583-24590.: The Birt-Hogg-Dube and tuberous sclerosis complex homologs have opposing roles in amino acid homeostasis in Schizosaccharomyces pombe. PUBMED:17556368 EPMC:17556368


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR021713

In yeast cells this family functions in the regulated delivery of Gap1p (a general amino acid permease) to the cell surface, perhaps as a component of a post-Golgi secretory-vesicle coat complex [PUBMED:9409822]. Birt-Hogg-Dube (BHD)4 syndrome is an autosomal dominant disorder characterised by hamartomas of skin follicles, lung cysts, spontaneous pneumothorax, and renal cell carcinoma. Folliculin is the protein from the BHD4 gene and is found to have no significant homology to any other human proteins. It is expressed in most tissues. These same symptoms also occur in TSC or tuberous sclerosis complex, suggesting that the same pathway is involved, and it is likely that the target is the down-stream Tor2 - an essential gene. Folliculin appears to bind Tor2, and down-regulation of Tor2 activity leads to up-regulation of nitrogen responsive genes including membrane transporters and amino acid permeases [PUBMED:17556368].

Domain organisation

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Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

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(20)
Full
(292)
Representative proteomes NCBI
(274)
Meta
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(45)
RP35
(80)
RP55
(143)
RP75
(195)
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  Seed
(20)
Full
(292)
Representative proteomes NCBI
(274)
Meta
(0)
RP15
(45)
RP35
(80)
RP55
(143)
RP75
(195)
Alignment:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(20)
Full
(292)
Representative proteomes NCBI
(274)
Meta
(0)
RP15
(45)
RP35
(80)
RP55
(143)
RP75
(195)
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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

HMM logo

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Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_3276 (release 23.0), ADDA_17305
Previous IDs: none
Type: Family
Author: Wood V, Coggill P
Number in seed: 20
Number in full: 292
Average length of the domain: 170.90 aa
Average identity of full alignment: 24 %
Average coverage of the sequence by the domain: 32.06 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.1 21.1
Trusted cut-off 22.4 21.4
Noise cut-off 20.7 20.7
Model length: 168
Family (HMM) version: 3
Download: download the raw HMM for this family

Species distribution

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